Package fr.ens.biologie.genomique.eoulsan.modules.singlecell

Class RSingleCellExperimentCreatorModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule

All Implemented Interfaces:

Module

public class RSingleCellExperimentCreatorModule
extends AbstractModule

This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.

Since:

2.3

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
RSingleCellExperimentCreatorModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
OutputPorts	getOutputPorts()	Get the output data format.
Set<Requirement>	getRequirements()	Get the requirements of the module.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getDescription, getParallelizationMode, getRequiredEoulsanVersion

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RSingleCellExperimentCreatorModule

public RSingleCellExperimentCreatorModule()

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

an set with DataFormat or null if the module does not produce any output data

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

getRequirements

public Set<Requirement> getRequirements()

Description copied from interface: Module

Get the requirements of the module.

Specified by:

getRequirements in interface Module

Overrides:

getRequirements in class AbstractModule

Returns:

a set with the requirements of the module

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task